Inferring introgression: Genomic study on hybridizing Darwin’s Finches highlights the importance of field observations

Explaining patterns of introgression required a thorough knowledge of the study system.

Yesterday I assisted in a field course on habitat analysis for ecologists. The students would visit an field site and explore different aspects of the ecosystem. In my section, we would walk through forest plot and try to identify common Dutch tree species. Due to the Corona-measures, most students had learned about these species in an online course, without hands-on experience in the field. And it showed. Some students struggled to identify the species at first. But once they knew which traits to focus on, they managed to identify most species correctly. This experience highlights the importance of fieldwork.

During my postdoc in Sweden, most of my colleagues worked on the genetics of the black-and-white flycatcher system: pied flycatcher (Ficedula hypoleuca) and collared flycatcher (F. albicollis). To my surprise, some colleagues had not seen these species in the wild and seemed uninterested in the natural history of these beautiful birds. They preferred to focus on abstract genetic concepts (which is also interesting). But how can you interpret the genetic data when you don’t know the ecology of the species? A recent paper in the journal Nature Ecology & Evolution illustrates the importance of knowing the ins and outs of your study system.

The pointed beak of the cactus finch (Geospiza scandens) © Mike’s Birds | Wikimedia Commons


Geospiza Finches

When I say “Peter and Rosemary Grant”, you will probably say “Darwin’s Finches”. Indeed, the Grants are known for their long-term study of these small passerines on the Galapagos Islands. On the island of Daphne Major, they documented hybridization between medium ground finch (Geospiza fortis) and cactus finch (G. scandens). Their meticulous study revealed that these species are converging morphologically: the long beaks of G. scandens became blunter and the robust beaks of G. fortis became more pointed. The change of beak morphology was greater in G. scandens, suggesting that genes are primarily flowing from G. fortis into G. scandens.

A recent genomic study confirmed this suggestion and went one step further. Sangeet Lamichhaney and his colleagues – including the Grants – compared the patterns of genetic exchange (i.e. introgression) for different parts of the genome. The genetic analyses pointed to extensive introgression of the autosomes (i.e. any chromosome that is not a sex chromosome) and the mitochondrial DNA, but not of the Z-chromosome.

The genetic analyses indicated introgression of the autosomes and of mtDNA, as shown by the position of SLB (G. scandens with blunt beak). On the Z-chromosome, this group of birds clusters with the other G. scandens samples. (Red = G. scandens, Blue = G. fortis). From Lamichhaney et al. (2020) Nature Ecology and Evolution


If you would show this result to my genetics-focused colleague in Sweden, she might attribute it to genetic incompatibilities on the sex chromosomes. And indeed, numerous other studies have found strong selection on sex-linked genes, contributing in reproductive isolation (check out this review on sex chromosomes and speciation). In this case, however, the ecology of the species is important. The field observations provided some crucial insights.

All female finches, including hybrid daughters, preferentially mate with males that sing the same song as their fathers’ song: mate choice is based on the imprinting of offspring on the parental morphology and song. The net result of this pattern of mating is the introgression of mtDNA and autosomal genes but few Z chromosomes from G. fortis to G. scandens. Hybrid females from these matings carry a G. scandens Z chromosome and cannot introgress any G. fortis Z chromosome. Hybrid sons, being relatively small, are at a disadvantage in competition with G. scandens males for high-quality territories and mates.

So, the reduced introgression on the Z-chromosome is not due to genetic incompatibilities, but can be explained by the behavior of the birds. The moral of this story: go into the field before you get into the lab.



Lamichhaney, S., Han, F., Webster, M. T., Grant, B. R., Grant, P. R., & Andersson, L. (2020). Female-biased gene flow between two species of Darwin’s finches. Nature Ecology & Evolution, 1-8.


This paper has been added to the Thraupidae page.

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